From 224fd1733ff5e5054fdd7bcd639ff4abd1e703bc Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 19 Dec 2021 13:02:02 -0800
Subject: [PATCH] improve aromatic bonds
- Don't detect aromatic bonds for rings < 5 atoms based on planarity
- Prefer atoms in aromatic rings as bond reference positions
---
CHANGELOG.md | 3 +++
src/mol-model/structure/structure/unit/rings.ts | 1 +
src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts | 4 ++--
src/mol-repr/structure/visual/bond-intra-unit-line.ts | 4 ++--
4 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index df9e74a1a..eb9fbc9ad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,6 +28,9 @@ Note that since we don't clearly distinguish between a public and private interf
- Support ``onBeforeUIRender`` to make sure initial UI works with custom presets and similar features.
- [Breaking] Removed ``createPlugin`` and ``createPluginAsync`` from ``mol-plugin-ui``
- Please use ``createPluginUI`` instead
+- Improve aromatic bonds handling
+ - Don't detect aromatic bonds for rings < 5 atoms based on planarity
+ - Prefer atoms in aromatic rings as bond reference positions
## [v3.0.0-dev.5] - 2021-12-16
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index 99501fc6d..519b57274 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -122,6 +122,7 @@ namespace UnitRing {
}
if (aromaticBondCount === 2 * ring.length) return true;
if (!hasAromaticRingElement) return false;
+ if (ring.length < 5) return false;
const ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring));
return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold;
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index abd5d82a7..6a7db3014 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -88,14 +88,14 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
if (aI > bI) [aI, bI] = [bI, aI];
if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI];
- const aR = elementRingIndices.get(aI);
+ const aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
let maxSize = 0;
for (let i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
const _bI = b[i];
if (_bI !== bI && _bI !== aI) {
if (aR) {
- const _bR = elementRingIndices.get(_bI);
+ const _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
if (!_bR) continue;
const size = arrayIntersectionSize(aR, _bR);
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-line.ts b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
index 1ad1fa45f..df34bfba5 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -61,14 +61,14 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
if (aI > bI) [aI, bI] = [bI, aI];
if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI];
- const aR = elementRingIndices.get(aI);
+ const aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
let maxSize = 0;
for (let i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
const _bI = b[i];
if (_bI !== bI && _bI !== aI) {
if (aR) {
- const _bR = elementRingIndices.get(_bI);
+ const _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
if (!_bR) continue;
const size = arrayIntersectionSize(aR, _bR);
--
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